Long Island Rail Road riders may soon have another reason to hate Monday mornings.

Starting tonight, the four heavily trafficked East River tunnels into Penn Station are getting a major overhaul that will shut some of them down every weekend for the next four years — a gargantuan project that has the potential to doom the start of the work week for thousands.

The MTA insists that the weekend megaproject to replace tracks and improve drainage will have little to no impact on riders — with one huge caveat.

The complex work, done in 55-hour intervals beginning Friday nights, must finish every Monday by 5 a.m. sharp — when hundreds of commuter trains start rolling into the city.

Every LIRR train into Penn Station uses those tunnels.

Even a relatively short delay in the workers’ vacating the tunnels could set off a chain reaction that would lead to severe backups throughout the system.

And that’s just one potential hiccup.

Any routine complication that forces even one of the tunnels to remain closed for longer than anticipated could set off the railroad equivalent of bumper-to-bumper traffic.

Amtrak, which owns the tunnels, is performing the work — a major source of concern among some officials.

“The Long Island rider’s fate is in the hands of some Amtrak supervisor taking orders from Washington,” groused MTA board member Charles Moerdler.

“I do not have confidence in Amtrak. Go look at New Jersey Transit; every day of the week, they have problems.”

Two major NJ Transit lines use Amtrak tracks.

Fellow MTA board member Mitchell Pally, who co-chairs the agency’s LIRR committee, was also dubious that Amtrak could pull off the job without impacting commuters.

“I’ll believe it when I see it,” Pally said.

“Those tunnels have been their responsibility for 40 years, and they haven’t done proper maintenance in 40 years.”

The LIRR runs 552 trains in and out of Penn Station on a typical weekday. Amtrak runs only 136, mainly to and from Boston.

“It’s not the Amtrak customers who will be inconvenienced,” Pally explained. “It will be our customers.”

Those customers were less than thrilled to hear about the project yesterday at Penn Station.

“In a perfect world, it sounds good, but one minor hiccup and all of the trains will be backed up,” said Ryan Lambert, 38, who commutes from Shirley.

Anna Ryan said she has had far too many problems dealing with LIRR delays to be optimistic.

“My husband and I are always late, and this will only make things worse,” she said.

In the first phase of the project, workers will be closing down only one tunnel.

But starting in 2012, two will be out of business every weekend.

Commuters will see light at the end of the tunnel project by 2015. It’s supposed to be completed sometime that year.

Weekend service could also take a serious hit, since there will be a very limited ability to shift trains around if a problem arises in one of the operational tunnels.

The MTA is working out a deal under which Amtrak could be penalized for not finishing on time, said LIRR President Helena E. Williams.

An Amtrak spokesman said the railroad has been in constant contact with the MTA to make sure the work doesn’t disrupt service.

It’s being done at the request of the MTA after a derailment in May revealed some serious drainage issues.